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<h1>Cell.h</h1><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment"> * Cell.h</span>
<a name="l00003"></a>00003 <span class="comment"> *</span>
<a name="l00004"></a>00004 <span class="comment"> *  Created on: Feb 28, 2011</span>
<a name="l00005"></a>00005 <span class="comment"> *      Author: wjfortin</span>
<a name="l00006"></a>00006 <span class="comment"> */</span>
<a name="l00007"></a>00007 <span class="preprocessor">#ifndef CELL_H_</span>
<a name="l00008"></a>00008 <span class="preprocessor"></span><span class="preprocessor">#define CELL_H_</span>
<a name="l00009"></a>00009 <span class="preprocessor"></span>
<a name="l00010"></a>00010 <span class="preprocessor">#include &lt;vector&gt;</span>
<a name="l00011"></a>00011 <span class="preprocessor">#include &quot;data/Molecule.h&quot;</span>
<a name="l00012"></a>00012 <span class="preprocessor">#include &quot;data/Protein.h&quot;</span>
<a name="l00013"></a>00013 <span class="preprocessor">#include &quot;data/DNA.h&quot;</span>
<a name="l00014"></a>00014 <span class="preprocessor">#include &quot;data/MRNA.h&quot;</span>
<a name="l00015"></a>00015 <span class="preprocessor">#include &quot;data/Interaction.h&quot;</span>
<a name="l00016"></a>00016 <span class="preprocessor">#include &quot;MersenneTwister.h&quot;</span>
<a name="l00017"></a>00017 <span class="preprocessor">#include &quot;Constants.h&quot;</span>
<a name="l00018"></a>00018 <span class="preprocessor">#include &lt;lemon/list_graph.h&gt;</span>
<a name="l00019"></a>00019 <span class="preprocessor">#include &quot;Trace.h&quot;</span>
<a name="l00020"></a>00020 <span class="preprocessor">#include &lt;fstream&gt;</span>
<a name="l00021"></a>00021 <span class="preprocessor">#include &lt;sys/stat.h&gt;</span>
<a name="l00022"></a>00022 <span class="preprocessor">#include &lt;sys/types.h&gt;</span>
<a name="l00023"></a>00023 
<a name="l00024"></a>00024 
<a name="l00025"></a>00025 <span class="preprocessor">#include &lt;typeinfo&gt;</span>
<a name="l00026"></a>00026 
<a name="l00027"></a>00027 <span class="keyword">using namespace </span>lemon;
<a name="l00028"></a>00028 <span class="keyword">using namespace </span>std;
<a name="l00029"></a>00029 
<a name="l00030"></a><a class="code" href="classCell.html">00030</a> <span class="keyword">class </span><a class="code" href="classCell.html">Cell</a> {
<a name="l00031"></a>00031 <span class="keyword">public</span>:
<a name="l00032"></a>00032         <a class="code" href="classCell.html#a394510643e8664cf12b5efaf5cb99f71">Cell</a>();
<a name="l00033"></a>00033         <span class="keyword">virtual</span> <a class="code" href="classCell.html#a9fa559f7a28e2b4336c6879ca09304d8">~Cell</a>();
<a name="l00034"></a>00034         <span class="keywordtype">int</span> <a class="code" href="classCell.html#a21d548d458486cb101c787ff34595848">nextGeneration</a>();
<a name="l00035"></a>00035         <span class="keywordtype">int</span> <a class="code" href="classCell.html#a1b9ffd156292e2412d44e2b0ea43c835">getScore</a>(<span class="keywordtype">int</span>);
<a name="l00036"></a>00036         <span class="keywordtype">int</span> <a class="code" href="classCell.html#a7b4cbc6fed25a9a8d5d4c5a60fe85590">getCellID</a>();
<a name="l00037"></a>00037         ListDigraph* equations;
<a name="l00038"></a>00038         ListDigraph::NodeMap&lt;Molecule*&gt;* vertexes;
<a name="l00039"></a>00039         ListDigraph::ArcMap&lt;Interaction*&gt;* edges;
<a name="l00040"></a>00040 
<a name="l00041"></a>00041         vector&lt;Protein*&gt; proteinList;
<a name="l00042"></a>00042 
<a name="l00043"></a>00043         ListDigraph::Node <a class="code" href="classCell.html#a6676a497230bcc7664b9ffd245c395b4">addProtein</a>(<span class="keywordtype">float</span>);
<a name="l00044"></a>00044         ListDigraph::Node <a class="code" href="classCell.html#a6676a497230bcc7664b9ffd245c395b4">addProtein</a>(<a class="code" href="classProtein.html">Protein</a>*);
<a name="l00045"></a>00045         ListDigraph::Node <a class="code" href="classCell.html#a51517080a4d784c1b825dd7bbe520368">addMRNA</a>(<span class="keywordtype">float</span>);
<a name="l00046"></a>00046         ListDigraph::Node <a class="code" href="classCell.html#a7d39f98796a73ac263a52550c99a15d8">addDNA</a>(<span class="keywordtype">float</span>);
<a name="l00047"></a>00047 
<a name="l00048"></a>00048         ListDigraph::Arc <a class="code" href="classCell.html#a1c787fc2fe52788c8271eb815b370aba">addInteraction</a>(ListDigraph::Node, ListDigraph::Node, <span class="keywordtype">float</span>, <span class="keywordtype">float</span>, <span class="keywordtype">float</span>, <span class="keyword">const</span> <span class="keywordtype">char</span>*);
<a name="l00049"></a>00049         ListDigraph::Arc <a class="code" href="classCell.html#a1c787fc2fe52788c8271eb815b370aba">addInteraction</a>(ListDigraph::Node, ListDigraph::Node, <a class="code" href="structQuantity.html">Quantity</a>*, <span class="keywordtype">float</span>, <span class="keywordtype">float</span>, <span class="keyword">const</span> <span class="keywordtype">char</span>*);
<a name="l00050"></a>00050 
<a name="l00051"></a>00051         <span class="keywordtype">int</span> <a class="code" href="classCell.html#ad316c047bcd04f6b4f0a3fe6cf3f2eaf">newComplex</a>();
<a name="l00052"></a>00052         <span class="keywordtype">int</span> <a class="code" href="classCell.html#a8ec1b55132525da1ae7bf7f05b9e4893">newBasic</a>();
<a name="l00053"></a>00053         <span class="keywordtype">int</span> <a class="code" href="classCell.html#a2d93a1672e574f231c86d86067b31f74">fwdRateChange</a>();
<a name="l00054"></a>00054         <span class="keywordtype">int</span> <a class="code" href="classCell.html#a3a80841a57d54309973dc947427f91f6">revRateChange</a>();
<a name="l00055"></a>00055         <span class="keywordtype">int</span> <a class="code" href="classCell.html#acec681969db4cc0fb80021a5613d8e8c">degRateChange</a>();
<a name="l00056"></a>00056         <span class="keywordtype">int</span> <a class="code" href="classCell.html#ac0159abe04ce33e168782e646a4424e3">newPostTransMod</a>();
<a name="l00057"></a>00057 
<a name="l00058"></a>00058         <span class="keywordtype">int</span> <a class="code" href="classCell.html#af8333316f26868a1f1cad1291c8770f4">histoneMod</a>();
<a name="l00059"></a>00059         <span class="keywordtype">int</span> <a class="code" href="classCell.html#a97385b8986611c19ff9f97597a33a6ff">newPromoter</a>();
<a name="l00060"></a>00060 
<a name="l00061"></a>00061         <span class="keywordtype">bool</span> <a class="code" href="classCell.html#a3184d63ac9ee1e4cb60b9fd38c870bf0">isComplexed</a>(<a class="code" href="classProtein.html">Protein</a>*, <a class="code" href="classProtein.html">Protein</a> *);
<a name="l00062"></a>00062 
<a name="l00063"></a>00063         <span class="keywordtype">int</span> cellID;
<a name="l00064"></a>00064 
<a name="l00065"></a>00065         <span class="keywordtype">void</span> <a class="code" href="classCell.html#ac165ee3b5920d5b4ac200ae6b016cea8">rungeKuttaEvaluate</a>(<span class="keywordtype">float</span>, <span class="keywordtype">float</span>);
<a name="l00066"></a>00066 
<a name="l00067"></a>00067 <span class="keyword">private</span>:
<a name="l00068"></a>00068 
<a name="l00069"></a>00069         ListDigraph::Node getRandomProtein();
<a name="l00070"></a>00070         ListDigraph::Node * degraded;
<a name="l00071"></a>00071         <span class="keywordtype">int</span> mutate();
<a name="l00072"></a>00072         vector&lt;Quantity*&gt; constants;
<a name="l00073"></a>00073         <span class="keywordtype">int</span> numGenerations;
<a name="l00074"></a>00074         <span class="keyword">static</span> <span class="keywordtype">int</span> cellCounter;
<a name="l00075"></a>00075         <a class="code" href="classMTRand.html">MTRand</a> r;
<a name="l00076"></a>00076         ListDigraph::Node nullNode;
<a name="l00077"></a>00077 
<a name="l00078"></a>00078         <span class="keywordtype">int</span> moleculeCount;
<a name="l00079"></a>00079 
<a name="l00080"></a>00080         ofstream mutationLog;
<a name="l00081"></a>00081 
<a name="l00082"></a>00082         <span class="keywordtype">float</span> rkDataLimit;
<a name="l00083"></a>00083         <span class="keywordtype">float</span> rkDataStep;
<a name="l00084"></a>00084 
<a name="l00085"></a>00085         <span class="keywordtype">void</span> cleanRkData(<span class="keywordtype">float</span>, <span class="keywordtype">float</span>);
<a name="l00086"></a>00086         <span class="keywordtype">void</span> outputRungeKuttaData();
<a name="l00087"></a>00087 
<a name="l00088"></a>00088 };
<a name="l00089"></a>00089 
<a name="l00090"></a>00090 <span class="preprocessor">#endif </span><span class="comment">/* CELL_H_ */</span>
</pre></div></div>
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